Mechanically stretched chromosomes as targets for high-resolution FISH mapping

Improvement of high-resolution fluorescence in situ hybridisation mapping on chromosomes of Brassica oleracea var. capitata

The low resolution of chromosome-based Fluorescence in situ hybridisation (FISH) mapping is primarily due to the structure of the plant cell wall and cytoplasm and the compactness of regular chromosomes, which represent a significant obstacle to FISH. In order to improve spatial resolution and signal detection sensitivity, we provide a reproducible method to generate high-quality extended chromosomes that are ~13 times as long as their pachytene counterparts. We demonstrate that proteinase K used in this procedure is crucial for stretching pachytene chromosomes of Brassica oleracea in the context of a modified Carnoy's II fixative (6:1:3, ethanol:chloroform:acetic acid). The quality of super-stretched chromosomes was assessed in several FISH experiments. FISH signals from both repetitive 5S rDNA and single-copy ARC1 on super-stretched chromosomes are brighter than those on other different types of chromosome due to enhanced accessibility to targets on stretched pachytene chromosomes. In conclusion, the resulting extended chromosomes are suitable for FISH mapping for repetitive DNA sequences and the localisation of a single-copy locus, and FISH performed on super-stretched chromosomes can achieve significantly higher sensitivity and spatial resolution than other chromosome-based FISH mapping techniques.

The expression of preaxial polydactyly is influenced by modifying genetic elements and is not maintained by chromosomal inversion in an avian biomedical model

Polydactyly (Po) is a common mutation found in many vertebrates. The UCD-Po.003 congenic chicken line was previously characterized for Po inheritance (autosomal dominant) and the mutation was mapped to chromosome 2p. Here, we describe for the first time the range and variability of the phenotype in this congenic line. Further, we studied the hypothesis that a chromosomal inversion was responsible for the maintenance of a large (6.3 Mb) candidate gene region. Fluorescence in situ hybridization employing BACs encompassing a 10.7-Mb region of GGA2p showed that the Po chromosome was normal, i.e. exhibits the wild-type BAC order. Continued fine-mapping along with a change in breeding strategy reduced the size of the causative region to 1.43 Mb. Recent research indicates that the cause of preaxial Po resides within a 794-bp highly conserved zone of polarizing activity regulatory sequence (ZRS) element located in intron 5 of the LMBR1 gene; however, the ZRS polymorphism of interest is found in some but not all breeds of polydactylous chicken. Therefore, we sequenced the ZRS in 101 heterozygous and 30 unaffected (wild-type) individuals to establish the relevance of this region to the Po condition in the UCD-Po.003 congenic line. A single point mutation (C/A at coordinate GGA2p: 8,414,121) within the ZRS segregated with carrier status. The polydactylous UCD-Silkie line also maintains this SNP in addition to a single base deletion. An inheritance analysis of the phenotypic variation in UCD-Po.003 suggests recessive epistasis as the mode of inheritance for the additional modifying genetic elements, residing outside the ZRS, to impact the preaxial polydactyl phenotype. These results contribute to our understanding of the cause of Po in an important vertebrate model.

Metaphase FISH on a chip: miniaturized microfluidic device for fluorescence in situ hybridization

Fluorescence in situ Hybridization (FISH) is a major cytogenetic technique for clinical genetic diagnosis of both inherited and acquired chromosomal abnormalities. Although FISH techniques have evolved and are often used together with other cytogenetic methods like CGH, PRINS and PNA-FISH, the process continues to be a manual, labour intensive, expensive and time consuming technique, often taking over 3 5 days, even in dedicated labs. We have developed a novel microFISH device to perform metaphase FISH on a chip which overcomes many shortcomings of the current laboratory protocols. This work also introduces a novel splashing device for preparing metaphase spreads on a microscope glass slide, followed by a rapid adhesive tape-based bonding protocol leading to rapid fabrication of the microFISH device. The microFISH device allows for an optimized metaphase FISH protocol on a chip with over a 20-fold reduction in the reagent volume. This is the first demonstration of metaphase FISH on a microfluidic device and offers a possibility of automation and significant cost reduction of many routine diagnostic tests of genetic anomalies.

Chromosome mapping of dragline silk genes in the genomes of widow spiders (Araneae, Theridiidae)

With its incredible strength and toughness, spider dragline silk is widely lauded for its impressive material properties. Dragline silk is composed of two structural proteins, MaSp1 and MaSp2, which are encoded by members of the spidroin gene family. While previous studies have characterized the genes that encode the constituent proteins of spider silks, nothing is known about the physical location of these genes. We determined karyotypes and sex chromosome organization for the widow spiders, Latrodectus hesperus and L. geometricus (Araneae, Theridiidae). We then used fluorescence in situ hybridization to map the genomic locations of the genes for the silk proteins that compose the remarkable spider dragline. These genes included three loci for the MaSp1 protein and the single locus for the MaSp2 protein. In addition, we mapped a MaSp1 pseudogene. All the MaSp1 gene copies and pseudogene localized to a single chromosomal region while MaSp2 was located on a different chromosome of L. hesperus. Using probes derived from L. hesperus, we comparatively mapped all three MaSp1 loci to a single region of a L. geometricus chromosome. As with L. hesperus, MaSp2 was found on a separate L. geometricus chromosome, thus again unlinked to the MaSp1 loci. These results indicate orthology of the corresponding chromosomal regions in the two widow genomes. Moreover, the occurrence of multiple MaSp1 loci in a conserved gene cluster across species suggests that MaSp1 proliferated by tandem duplication in a common ancestor of L. geometricus and L. hesperus. Unequal crossover events during recombination could have given rise to the gene copies and could also maintain sequence similarity among gene copies over time. Further comparative mapping with taxa of increasing divergence from Latrodectus will pinpoint when the MaSp1 duplication events occurred and the phylogenetic distribution of silk gene linkage patterns.

A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk

There is a complex relationship between the evolution of segmental duplications and rearrangements associated with human disease. We performed a detailed analysis of one region on chromosome 16p12.1 associated with neurocognitive disease and identified one of the largest structural inconsistencies with the human reference assembly. Various genomic analyses show that all examined humans are homozygously inverted relative to the reference genome for a 1.1-Mbp region on 16p12.1. We determined that this assembly discrepancy stems from two common structural configurations with worldwide frequencies of 17.6% (S1) and 82.4% (S2). This polymorphism arose from the rapid integration of segmental duplications, precipitating two local inversions within the human lineage over the last 10 million years. The two human haplotypes differ by 333 kbp of additional duplicated sequence present in S2 but not in S1. Importantly, we show that the S2 configuration harbors directly oriented duplications specifically predisposing this chromosome to disease rearrangement.

Super-stretched pachytene chromosomes for fluorescence in situ hybridization mapping and immunodetection of DNA methylation

Meiotic pachytene chromosome-based fluorescence in situ hybridization (FISH) mapping is one of the most important tools in plant molecular cytogenetic research. Here we report a simple technique that allows stretching of pachytene chromosomes of maize to up to at least 20 times their original size. A modified Carnoy's II fixative (6:1:3 ethanol:chloroform:acetic acid) was used in the procedure, and proved to be key for super-stretching of pachytene chromosomes. We demonstrate that super-stretched pachytene chromosomes provide unprecedented resolution for chromosome-based FISH mapping. DNA probes separated by as little as 50 kb can be resolved on super-stretched chromosomes. A combination of FISH with immunofluorescent detection of 5-methyl cytosine on super-stretched pachytene chromosomes provides a powerful tool to reveal DNA methylation of specific chromosomal domains, especially those associated with highly repetitive DNA sequences.

Regulation of vascular inflammation and remodeling by ETS factors

The ETS (E26 Transformation-specific Sequence) factors are comprised of a family of transcription factors that share a highly conserved DNA binding domain. Although originally described for their role as protooncogenes in the development of several types of human cancer, they have subsequently been shown to regulate a wide variety of biological processes including cellular growth and differentiation under normal and pathological conditions. As transcription factors, they can either function as activators or repressors of gene expression. Several ETS family members are expressed in cells of vascular origin, including endothelial cells and vascular smooth muscle cells, where they regulate the expression of a number of vascular-specific genes. In the past few years, emerging evidence supports a novel role for selected ETS family members in the regulation of vascular inflammation and remodeling. ETS factor expression can be induced by proinflammatory cytokines, growth factors, and vasoactive peptides. Examples of some of the target genes regulated by ETS factors include adhesion molecules, chemokines, and matrix metalloproteinases. Targeted disruption of selected ETS family members such as Ets-1 in mice is associated with marked reductions in the recruitment of inflammatory cells and vascular remodeling in response to systemic administration of the vasoactive peptide angiotensin II. The purpose of this review is to provide an overview of recent advances that have been made in defining a role for selected members of the ETS transcription factor family in the regulation of vascular-specific gene expression, vascular inflammation, and remodeling.

Segmental duplications flank the multiple sclerosis locus on chromosome 17q

Large chromosomal rearrangements, duplications, and inversions are relatively common in mammalian genomes. Here we report interesting features of DNA strands flanking a Multiple Sclerosis (MS) susceptibility locus on Chromosome 17q24. During the positional cloning process of this 3-Mb locus, several markers showed a radiation hybrid clone retention rate above the average (1.8-fold), suggestive for the existence of duplicated sequences in this region. FISH studies demonstrated multiple signals with three of the tested regional BACs, and 24 BACs out of 187 showed evidence for duplication in shotgun sequence comparisons of the 17q22-q24 region. Specifically, the MS haplotype region proved to be flanked by palindromic sequence stretches and by long segmental intrachromosomal duplications in which highly homologous DNA sequences (>96% identity) are present at both ends of the haplotype. Moreover, the 3-Mb DNA segment, flanked by the duplications, is inverted in the mouse genome when compared with the orientation in human and chimp. The segmental duplication architecture surrounding the MS locus raises the possibility that a nonallelic homologous recombination between duplications could affect the biological activity of the regional genes, perhaps even contributing to the genetic background of MS.

A novel interspersed type of organization of satellite DNAs in Tribolium madens heterochromatin

Analysis of arrangement of satellite DNA sequences in Tribolium madens (Insecta, Coleoptera) by Southern analysis of pulsed-field blots and two colour FISH on extended chromosomes and DNA fibres revealed a novel type of heterochromatin organization. Two satellite DNAs, distributed over the whole pericentromeric heterochromatin of all chromosomes form clusters, ranging in size from 150 kb up to several Mb. Within the clusters, both satellites are in the form of highly interspersed, short homogeneous arrays which vary in size with a lowest length limit of only few kb. The longest arrays composed of a single satellite are relatively short, up to 70 kb for satellite I, and up to 45 kb for satellite II. Only a small fraction of about 15% of satellite II is organized in long tandem repeats, while the rest is in the form of only a few repeats intermingled with satellite I. The results indicate that large clusters composed of interspersed arrays of both satellites represent a major component of T. madens heterochromatin, which is mostly devoid of long regions of other sequences. The same organizational pattern probably also includes a region of the functional centromere. We propose that such an organizational pattern of DNA sequences in heterochromatin might be common in genomes characterized by a high rate of interchromosomal exchange. This pattern of organization is different from that in other animal as well as plant species analysed up to now, in which every satellite in heterochromatin is organized in a small number of large separate domains.

High resolution free chromatin/DNA fiber fluorescent in situ hybridization

High resolution chromatin/DNA fiber fluorescent in situ hybridisation (FISH) is a powerful system for physical mapping and genome research. With direct visualisation of molecular probes along released chromatin or DNA fiber, fiber FISH has become the method of choice to order genes or DNA markers within chromosomal regions of interest. Combined with DNA-protein in situ codetection fiber FISH shall play a more important role for analysis of genome function. In this paper the concept and technical developments of fiber FISH are reviewed with the emphasis of comparison on the various protocols. Future challenges are also discussed along with the highlights of the successful applications achieved by fiber FISH methodology.

The Genome Sequence DataBase (GSDB): improving data quality and data access

In 1997 the primary focus of the Genome Sequence DataBase (GSDB; www. ncgr.org/gsdb ) located at the National Center for Genome Resources was to improve data quality and accessibility. Efforts to increase the quality of data within the database included two major projects; one to identify and remove all vector contamination from sequences in the database and one to create premier sequence sets (including both alignments and discontiguous sequences). Data accessibility was improved during the course of the last year in several ways. First, a graphical database sequence viewer was made available to researchers. Second, an update process was implemented for the web-based query tool, Maestro. Third, a web-based tool, Excerpt, was developed to retrieve selected regions of any sequence in the database. And lastly, a GSDB flatfile that contains annotation unique to GSDB (e.g., sequence analysis and alignment data) was developed. Additionally, the GSDB web site provides a tool for the detection of matrix attachment regions (MARs), which can be used to identify regions of high coding potential. The ultimate goal of this work is to make GSDB a more useful resource for genomic comparison studies and gene level studies by improving data quality and by providing data access capabilities that are consistent with the needs of both types of studies.

The order and transcriptional orientation of the human COL13A1 and P4HA genes on chromosome 10 long arm determined by high-resolution FISH

The genes for type XIII collagen (COL13A1) and prolyl 4-hydroxylase (P4HA) were previously assigned to human chromosome 10q by radioactive in situ hybridization. Here we have applied fluorescence in situ hybridization combined with targets representing different levels of resolution to determine, first, the order of these genes along chromosome 10; second, their transcriptional orientation; and third, the distance between these genes. The order along the chromosome was determined to be centromere-COL13A1-P4HA-telomere using mechanically stretched chromosomes. By combining the data from stretched chromosomes and interphase nuclei, we found that the transcriptional orientation were tail to tail (COL13A1 3'-3' P4HA). The distance between these genes was measured by fiber FISH to be approximately 550 kb.

High-resolution physical and transcriptional mapping of the autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy locus on chromosome 21q22.3 by FISH

Autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED, PGD type I) is an autosomal recessive disease enriched in the Finnish population. Previously, we have assigned APECED to a 2.6-cM interval on chromosome 21q22.3 by linkage analysis in 14 Finnish families. This subtelomeric region of 21q22.3 seems to have sequence features resulting in its under-representation in large insert genomic libraries, and only a few large insert clones have been available for positional cloning to date. Here, we report the refined localization of the APECED gene and a visual physical map of 800 kb covering the critical chromosomal region for the gene. In the construction of the physical map, the recently developed fiber FISH techniques were essential for the orientation of the cosmid PI, PAC, and BAC clones in relation to each other. We also localized two cDNAs within this genomic region by fiber FISH combined with the highly sensitive tyramide-based detection method. These data will facilitate the final cloning of the APECED gene and any other novel gene in this complex genomic region.

Utilization of FISH in positional cloning: an example on 13q22

In positional cloning the initial assignment of a gene to a specific chromosomal locus is followed by physical mapping of the critical region. The construction of a high-resolution physical map still involves considerable effort. However, new high-resolution fluorescence in situ hybridization (FISH) techniques have facilitated this process substantially. Here we summarize a strategy that combines a spectrum of FISH techniques [metaphase, interphase, mechanically stretched chromosomes (MSCs), and fiber-FISH on free chromatin] for the construction and characterization of a high-resolution physical map for a positional cloning project. The chromosomal region 13q22, containing the locus of the variant form of the neuronal ceroid lipofuscinosis (vLINCL, CLN5) disease, serves here as an example for this process. We used metaphase FISH to exclude positionally a candidate gene, to refine the locus to 13q22, and to analyze the possible chimerism of the YACs in the region. Both metaphase and interphase FISH techniques were applied to determine the low-resolution distances between the restricting markers. FISH using MSCs confirmed the centromeric-telomeric order of the clones and facilitated the estimation of the size of the gaps between the clones. Finally, fiber-FISH was found to be the method of choice for the construction of an accurate high-resolution map of the contig established over the restricted region. Thus, FISH techniques in combination with genetic mapping data enabled the refinement of the initial 4-cM region to a high-resolution map of only 400 kb in length. Here the FISH strategy replaced the need for many laborious traditional physical mapping methods, e.g., pulsed-field gel electrophoresis.

High-resolution fluorescence in situ hybridization: a new approach in genome mapping

Mapping of the human genome has been a global effort utilizing both genetic and physical mapping techniques. One approach which has greatly facilitated the physical mapping of the human genome is fluorescence in situ hybridization (FISH). Although FISH is by now a well-established technology, new recently developed modifications have enabled an easier use and higher resolution. The high-resolution FISH techniques have given a special impact in positional cloning: searching the functional gene from a chromosomal area where the gene has been genetically localized. New high-resolution FISH techniques include hybridization of probes to free chromatin, DNA fibres or mechanically stretched chromosomes. These targets have widened the resolution of FISH to detect distances from the traditional cytogenetic resolution level down to a resolution of a few kilobases. They also have significantly speeded up high-resolution physical mapping and thus made the search of new disease genes easier.